SMTL ID : 6t05.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 18 (DHU_DC1_048)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, P.105 Ligands: M6H.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.37, A:N.37, A:N.38, A:N.41 Water bridges: A:S.36, A:N.38, A:R.78 SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 3 residues within 4Å: Chain A: S.93, H.94, H.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:S.93, A:G.96, A:G.96 Salt bridges: A:H.94 SO4.4: 3 residues within 4Å: Chain A: R.78, R.149, D.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.78 Salt bridges: A:R.78

2 x M6H: 2-(phenylmethyl)imidazolidine(Non-covalent)

M6H.5: 10 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, M.108, M.112, L.113 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.51, A:L.54, A:L.113, A:L.113 Hydrogen bonds: A:N.41, A:S.52 M6H.6: 2 residues within 4Å: Chain A: H.101, W.102 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments. Acs Chem.Biol. (2020)

Release Date

2020-03-04

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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